tbuckley/cabot-search huggingface dataset:
Prevalence of injecting drug use and HIV, hepatitis B, and hepatitis C in people who inject drugs in the Eastern Mediterranean region: a systematic review and meta-analysis
Authors: Ardavan Mohammad Aghaei, Jaleh Gholami, Arshiya Sangchooli, Yasna Rostam-Abadi, Sogol Olamazadeh, Maryam Ardeshir, Shahab Baheshmat, Behrang Shadloo, Mahshid Taj, Khalid Saeed, Afarin Rahimi-Movaghar
Journal: The Lancet Global Health (2023)

BackgroundConsiderable disease burden is attributed to injecting drug use (IDU). This regional systematic review and meta-analysis aimed to assess the prevalence of IDU and the characteristics of people who inject drugs in the 22 countries of the WHO Eastern Mediterranean region.MethodsWe conducted a systematic review and meta-analysis on the prevalence of IDU, estimation of the population size of people who inject drugs, the characteristics of people who inject drugs, commonly injected drugs, the prevalence of HIV, hepatitis C virus, and hepatitis B virus in people who inject drugs, and opioid agonist treatment and needle and syringe programme services. We searched PubMed, Web of Science, Scopus, Embase, and the Index Medicus for the Eastern Mediterranean Region for documents published between Jan 1, 2010, and April 17, 2022, with no language restrictions. We also searched government reports, civil society information, and UN websites and databases for grey literature published between Jan 1, 2010, and April 17, 2022. Documents were eligible if they reported or estimated an indicator of interest, or reported enough data to permit calculation of the indicator. We extracted data from the eligible documents and calculated national and regional estimates.FindingsWe identified 38 283 documents and included 201 documents in the systematic review. A total of 115 documents were included for the four outcomes for which meta-analyses were performed. The number of people who inject drugs was estimated as 864 597 (95% CI 641 909–1 205 255), amounting to a prevalence of 20·0 per 10 000 adults (95% CI 14·9–27·9) in the region. Among people who inject drugs, the prevalence of HIV was estimated as 19·22% (95% CI 12·86–26·36), hepatitis C virus as 44·82% (29·32–61·16), and hepatitis B virus as 2·66% (0·84–7·26). Countries varied greatly regarding the variables of interest and the availability of relevant data. Nine countries provided needle and syringe programme services and seven countries provided opioid agonist treatment services, mostly with very low, low, or unclear coverage.InterpretationThe prevalence of IDU in the Eastern Mediterranean region is lower than the global mean, particularly among women. The HIV infection rate is higher than the global mean, and the hepatitis C virus infection rate is lower than the global mean. Harm-reduction services are underdeveloped. Data collection on IDU and provision of services need improvement in the region.FundingWorld Health Organization.TranslationsFor the Arabic, Farsi and French translations of the abstract see Supplementary Materials section.
Beyond Supervised Learning for Pervasive Healthcare
Authors: Xiao Gu, Fani Deligianni, Jinpei Han, Xiangyu Liu, Wei Chen, Guang-Zhong Yang, Benny Lo
Journal: IEEE Reviews in Biomedical Engineering (2023)

The integration of machine/deep learning and sensing technologies is transforming healthcare and medical practice. However, inherent limitations in healthcare data, namely scarcity, quality, and heterogeneity, hinder the effectiveness of supervised learning techniques which are mainly based on pure statistical fitting between data and labels. In this article, we first identify the challenges present in machine learning for pervasive healthcare and we then review the current trends beyond fully supervised learning that are developed to address these three issues. Rooted in the inherent drawbacks of empirical risk minimization that underpins pure fully supervised learning, this survey summarizes seven key lines of learning strategies, to promote the generalization performance for real-world deployment. In addition, we point out several directions that are emerging and promising in this area, to develop data-efficient, scalable, and trustworthy computational models, and to leverage multi-modality and multi-source sensing informatics, for pervasive healthcare.
Fecal virome transplantation is sufficient to alter fecal microbiota and drive lean and obese body phenotypes in mice
Authors: Joshua M. Borin, Roland Liu, Yanhan Wang, Tsung-Chin Wu, Jessica Chopyk, Lina Huang, Peiting Kuo, Chandrabali Ghose, Justin R. Meyer, Xin M. Tu, Bernd Schnabl, David T. Pride
Journal: Gut Microbes (2023)

The gastrointestinal microbiome plays a significant role in modulating numerous host processes, including metabolism. Prior studies show that when mice receive fecal transplants from obese donors on high-fat diets (HFD) (even when recipient mice are fed normal diets after transplantation), they develop obese phenotypes, demonstrating the prominent role that gut microbiota play in determining lean and obese phenotypes. While much of the credit has been given to gut bacteria, the impact of gut viruses on these phenotypes is understudied. To address this shortcoming, we gavaged mice with viromes isolated from donors fed HFD or normal chow over a 4-week study. By characterizing the gut bacterial biota via 16S rRNA amplicon sequencing and measuring mouse weights over time, we demonstrate that transplanted viruses affect the gut bacterial community, as well as weight gain/loss. Notably, mice fed chow but gavaged with HFD-derived viromes gained more weight than their counterparts receiving chow-derived viromes. The converse was also true: mice fed HFD but gavaged with chow-derived viromes gained less weight than their counterparts receiving HFD-derived viromes. Results were replicated in two independent experiments and phenotypic changes were accompanied by significant and identifiable differences in the fecal bacterial biota. Due to methodological limitations, we were unable to identify the specific bacterial strains responsible for respective phenotypic changes. This study confirms that virome-mediated perturbations can alter the fecal microbiome in vivo and indicates that such perturbations are sufficient to drive lean and obese phenotypes in mice.
Endoscopic ultrasound-guided choledochoduodenostomy using single-step lumen-apposing metal stents for primary drainage of malignant distal biliary obstruction (SCORPION-p): a prospective pilot study
Authors: Rogier P. Voermans, Roy L. J. Van Wanrooij, Jeska A. Fritzsche, Paul Fockens, Marc G. Besselink, Olivier R. Busch, Freek Daams, Nahid S. M. Montazeri, Johanna W. Wilmink
Journal: Endoscopy (2023)

This study aimed to assess the safety and feasibility of endoscopic ultrasound-guided choledochoduodenostomy (EUS-CDS) using a lumen-apposing metal stent (LAMS) as a primary drainage strategy in patients with distal malignant biliary obstruction (MBO).
Women living with HTLV-1 should have the opportunity to make informed decisions on prevention of mother-to-child transmission
Authors: Carolina Rosadas, Kátia Senna, Milene da Costa, Tatiane Assone, Jorge Casseb, Youko Nukui, Lucy Cook, Lívia Mariano, Bernardo Galvão-Castro, Maria Fernanda Rios Grassi, Augusto Cesar Penalva de Oliveira, Adele Caterino-de-Araujo, Bassit Malik, Ney Boa-Sorte, Paula Peixoto, Marzia Puccioni-Sohler, Marisa Santos, Graham Philip Taylor
Journal: The Lancet Global Health (2023)
Acetylation of the NS3 helicase by KAT5γ is essential for flavivirus replication
Authors: Taryn Serman, Cindy Chiang, GuanQun Liu, Zuberwasim Sayyad, Shanti Pandey, Meta Volcic, Haejeong Lee, Santoshi Muppala, Dhiraj Acharya, Christopher Goins, Shaun R. Stauffer, Konstantin M.J. Sparrer, Michaela U. Gack
Journal: Cell Host & Microbe (2023)
Reply: Confounding in Mendelian randomisation studies
Authors: Carl J. Reynolds, Cosetta Minelli
Journal: European Respiratory Journal (2023)

<h3>Tweetable abstract</h3> <b>Mendelian randomisation (MR) overcomes classical confounding issues that beset observational studies. "Horizontal" but not "vertical" pleiotropy can bias MR study findings but we found no evidence that it was present in our MR analysis of GORD on IPF.</b>https://bit.ly/3Jn7aeq
From the sound of breathing to the sound of distress: implications for dyspnoeic patients and their caregivers
Authors: Nathalie Nion, Laure Serresse, Sophie Lavault, Thomas Similowski
Journal: European Respiratory Journal (2023)

<h3>Tweetable abstract</h3> <b>Hearing someone having trouble breathing induces emotions and a mixture of empathetic solicitude and distress, with consequences on the observer9s feelings and attitudes</b>https://bit.ly/3Cxp8a1
Correction: MIR22HG acts as a tumor suppressor via TGFβ/SMAD signaling and facilitates immunotherapy in colorectal cancer
Authors: Juan Xu, Tingting Shao, Mingxu Song, Yunjin Xie, Jialiang Zhou, Jiaqi Yin, Na Ding, Haozhe Zou, Yongsheng Li, Jiwei Zhang
Journal: Molecular Cancer (2023)

it to the correct one.The other elements of the figure remain the same, and the interpretation of the results remains unchanged.
The Growing Role of Technology in the Care of Older Adults With Diabetes
Authors: Elbert S. Huang, Alan Sinclair, Paul R. Conlin, Tali Cukierman-Yaffe, Irl B. Hirsch, Megan Huisingh-Scheetz, Anna R. Kahkoska, Lori Laffel, Alexandra K. Lee, Sei Lee, Kasia Lipska, Graydon Meneilly, Naushira Pandya, Monica E. Peek, Anne Peters, Richard E. Pratley, Diana Sherifali, Elena Toschi, Guillermo Umpierrez, Ruth S. Weinstock, Medha Munshi
Journal: Diabetes Care (2023)

The integration of technologies such as continuous glucose monitors, insulin pumps, and smart pens into diabetes management has the potential to support the transformation of health care services that provide a higher quality of diabetes care, lower costs and administrative burdens, and greater empowerment for people with diabetes and their caregivers. Among people with diabetes, older adults are a distinct subpopulation in terms of their clinical heterogeneity, care priorities, and technology integration. The scientific evidence and clinical experience with these technologies among older adults are growing but are still modest. In this review, we describe the current knowledge regarding the impact of technology in older adults with diabetes, identify major barriers to the use of existing and emerging technologies, describe areas of care that could be optimized by technology, and identify areas for future research to fulfill the potential promise of evidence-based technology integrated into care for this important population.
Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus
Authors: David B. Sacks, Mark Arnold, George L. Bakris, David E. Bruns, Andrea R. Horvath, Åke Lernmark, Boyd E. Metzger, David M. Nathan, M. Sue Kirkman
Journal: Diabetes Care (2023)

BACKGROUND Numerous laboratory tests are used in the diagnosis and management of diabetes mellitus. The quality of the scientific evidence supporting the use of these assays varies substantially. APPROACH An expert committee compiled evidence-based recommendations for laboratory analysis in screening, diagnosis, or monitoring of diabetes. The overall quality of the evidence and the strength of the recommendations were evaluated. The draft consensus recommendations were evaluated by invited reviewers and presented for public comment. Suggestions were incorporated as deemed appropriate by the authors (see Acknowledgments). The guidelines were reviewed by the Evidence Based Laboratory Medicine Committee and the Board of Directors of the American Association for Clinical Chemistry and by the Professional Practice Committee of the American Diabetes Association. CONTENT Diabetes can be diagnosed by demonstrating increased concentrations of glucose in venous plasma or increased hemoglobin A1c (HbA1c) in the blood. Glycemic control is monitored by the people with diabetes measuring their own blood glucose with meters and/or with continuous interstitial glucose monitoring (CGM) devices and also by laboratory analysis of HbA1c. The potential roles of noninvasive glucose monitoring, genetic testing, and measurement of ketones, autoantibodies, urine albumin, insulin, proinsulin, and C-peptide are addressed. SUMMARY The guidelines provide specific recommendations based on published data or derived from expert consensus. Several analytes are found to have minimal clinical value at the present time, and measurement of them is not recommended.
LONRF2 is a protein quality control ubiquitin ligase whose deficiency causes late-onset neurological deficits
Authors: Dan Li, Yoshikazu Johmura, Satoru Morimoto, Miyuki Doi, Keiko Nakanishi, Manabu Ozawa, Yuji Tsunekawa, Akane Inoue-Yamauchi, Hiroya Naruse, Takashi Matsukawa, Yukio Takeshita, Naoki Suzuki, Masashi Aoki, Ayumi Nishiyama, Xin Zeng, Chieko Konishi, Narumi Suzuki, Atsuya Nishiyama, Alexander Stephen Harris, Mariko Morita, Kiyoshi Yamaguchi, Yoichi Furukawa, Kenta Nakai, Shoji Tsuji, Satoshi Yamazaki, Yuji Yamanashi, Shoichi Shimada, Takashi Okada, Hideyuki Okano, Tatsushi Toda, Makoto Nakanishi
Journal: Nature Aging (2023)
Anticancer Initiative Targets Areas of Poverty
Journal: Cancer Discovery (2023)

The NCI and NIH awarded $50 million over 5 years to five university-based centers to conduct research and implement programs aimed at improving how people with cancer fare in low-income areas. Centers participating in the Persistent Poverty Initiative will expand research in high-poverty areas and engage patients in cancer prevention through lifestyle changes, such as smoking cessation, healthy eating, and physical activity.
Golnaz Vahedi: My environment enables me to achieve impossible goals
Authors: Lucie Van Emmenis
Journal: The Journal of Experimental Medicine (2023)

Golnaz Vahedi is an associate professor of genetics at the Perelman School of Medicine, University of Pennsylvania. Golnaz runs a multidisciplinary lab that uses cutting-edge computational and experimental approaches to understand the molecular mechanisms by which genomic information in immune cells is interpreted in normal development and during immune-mediated diseases. We talked about her diverse scientific background, the benefits of integrating molecular biology and immunology, and the importance of staying positive in academia.
ThPOK is a critical multifaceted regulator of myeloid lineage development
Authors: Jayati Basu, Andre Olsson, Kyle Ferchen, Elizaveta K. Titerina, Kashish Chetal, Emmanuelle Nicolas, Philip Czyzewicz, Dmitry Levchenko, Lu Ge, Xiang Hua, H. Leighton Grimes, Nathan Salomonis, Dietmar J. Kappes
Journal: Nature Immunology (2023)
New insights into programmed cell death protein 1 blockade-associated cutaneous immune-related adverse events
Authors: Goran Micevic, Andrew Daniels, Richard A Flavell
Journal: British Journal of Dermatology (2023)

Cutaneous side-effects associated with immune checkpoint blockade occur in more than half of patients treated with CTLA-4 and PD-1 inhibitors, and are frequently encountered by dermatologists. The molecular mechanism of cutaneous side-effects is incompletely understood but holds important clues about immune tolerance and the antitumor immune response in the skin. A new landmark study published in Nature suggests a critical functional role for the checkpoint receptor PD-1 in restraining self-reactive T cells, which could help explain how some checkpoint-associated cutaneous side-effects arise.
Liquid Biopsies with Circulating Plasma HPV–DNA Measurements—A Clinically Applicable Surveillance Tool for Patients with HPV-Positive Oropharyngeal Cancer
Authors: Kathrine K. Jakobsen, Simone K. Bendtsen, Niels Pallisgaard, Jeppe Friborg, Giedrius Lelkaitis, Christian Grønhøj, Christian von Buchwald
Journal: Clinical Cancer Research (2023)

To evaluate the accuracy of cell-free human papillomavirus-DNA (cfHPV-DNA) measurements in liquid biopsies in predicting disease in patients with HPV-positive/p16-positive (HPV+/p16+) oropharyngeal squamous cell carcinoma (OPSCC).This was a prospective cohort study. Plasma samples were collected before treatment, serially after curative intended therapy at follow-up visits 2 weeks, and 6, 9, 12, 18, 24, and 30 months after treatment. A droplet digital PCR assay comprising eight HPV genotypes was used. HPV genotypes found in plasma and tumor tissue were compared. We correlated biopsy- or imaging-verified tumor progression to cfHPV-DNA in follow-up samples.We enrolled 72 patients with HPV+/p16+ OPSCC. Baseline sensitivity for cfHPV-DNA detection was 97.2% (95% confidence interval, 90.3%-99.6%). CfHPV-DNA copy number/milliliter plasma correlated with tumor stage. We found a 100% concordance between HPV genotype in tumor tissue and plasma. Fifty-four patients were followed with serial blood samples for a median of 19.7 months (interquartile range, 13.5-25.5 months). Forty-one patients had undetectable plasma cfHPV-DNA in all follow-up samples, and none developed recurrences. Thirteen patients were classified as cfHPV-DNA-positive in a follow-up plasma sample. Of these, five patients developed a recurrence, and three had residual cancer. It was possible to detect cfHPV-DNA in plasma 97 to 166 days prior to the proven recurrence.To our knowledge, to date, our study, comprising the largest study of patients with HPV+/p16+ OPSCC, using an ultrasensitive multiplex HPV gene panel, revealed a high sensitivity of cfHPV-DNA detection in the liquid biopsies. We recommend serial plasma HPV samples for clinical monitoring of patients with HPV+/p16+ OPSCC.
A prospective multicenter study to examine the impact of acquired and genetic predictors on Hepatocellular carcinoma risk in patients with advanced NAFLD: first report
Authors: Serena Pelusi, Cristiana Bianco, Luisa Ronzoni, Alessandro Cherubini, Ilaria Marini, Francesco Malvestiti, Roberta D’Ambrosio, Anna Ludovica Fracanzani, Annalisa Cespiati, Giorgio Soardo, Stephanie Pivetta, Luca Miele, Antonio Liguori, Elisabetta Bugianesi, Chiara Rosso, Salvatore Petta, Grazia Pennisi, Umberto Vespasiani Gentilucci, Federica Tavaglione, Alessandro Federico, Francesco Paolo Russo, Paola Zanaga, Mario Masarone, Daniele Prati, Luca Valenti
Journal: Journal of Hepatology (2023)
Executive Summary: Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus
Authors: David B. Sacks, Mark Arnold, George L. Bakris, David E. Bruns, Andrea R. Horvath, Åke Lernmark, Boyd E. Metzger, David M. Nathan, M. Sue Kirkman
Journal: Diabetes Care (2023)

BACKGROUND Numerous laboratory tests are used in the diagnosis and management of patients with diabetes mellitus. The quality of the scientific evidence supporting the use of these assays varies substantially. An expert committee compiled evidence-based recommendations for laboratory analysis in patients with diabetes. The overall quality of the evidence and the strength of the recommendations were evaluated. The draft consensus recommendations were evaluated by invited reviewers and presented for public comment. Suggestions were incorporated as deemed appropriate by the authors (see Acknowledgments in the full version of the guideline). The guidelines were reviewed by the Evidence Based Laboratory Medicine Committee and the Board of Directors of the American Association for Clinical Chemistry and by the Professional Practice Committee of the American Diabetes Association. CONTENT Diabetes can be diagnosed by demonstrating increased concentrations of glucose in venous plasma or increased hemoglobin A1c (HbA1c) in the blood. Glycemic control is monitored by the patients measuring their own blood glucose with meters and/or with continuous interstitial glucose monitoring devices and also by laboratory analysis of HbA1c. The potential roles of noninvasive glucose monitoring; genetic testing; and measurement of ketones, autoantibodies, urine albumin, insulin, proinsulin, and C-peptide are addressed. SUMMARY The guidelines provide specific recommendations based on published data or derived from expert consensus. Several analytes are found to have minimal clinical value at the present time, and measurement of them is not recommended.
De-escalation or abbreviation of dual antiplatelet therapy in acute coronary syndromes and percutaneous coronary intervention: a Consensus Statement from an international expert panel on coronary thrombosis
Authors: Diana A. Gorog, Jose Luis Ferreiro, Ingo Ahrens, Junya Ako, Tobias Geisler, Sigrun Halvorsen, Kurt Huber, Young-Hoon Jeong, Eliano P. Navarese, Andrea Rubboli, Dirk Sibbing, Jolanta M. Siller-Matula, Robert F. Storey, Jack W. C. Tan, Jurrien M. ten Berg, Marco Valgimigli, Christophe Vandenbriele, Gregory Y. H. Lip
Journal: Nature Reviews Cardiology (2023)
Effect of onchocerciasis elimination measures on the incidence of epilepsy in Maridi, South Sudan: a 3-year longitudinal, prospective, population-based study
Authors: Stephen Raimon Jada, Luís-Jorge Amaral, Thomson Lakwo, Jane Y Carter, Jacopo Rovarini, Yak Yak Bol, Makoy Yibi Logora, Amber Hadermann, Adrian Hopkins, Joseph N Siewe Fodjo, Robert Colebunders
Journal: The Lancet Global Health (2023)
Autoimmunity to synovial extracellular matrix proteins in patients with postinfectious Lyme arthritis
Authors: Korawit Kanjana, Klemen Strle, Robert B. Lochhead, Annalisa Pianta, Laura M. Mateyka, Qi Wang, Sheila L. Arvikar, David E. Kling, Cameron A. Deangelo, Lucy Curham, Alan G. Barbour, Catherine E. Costello, James J. Moon, Allen C. Steere
Journal: Journal of Clinical Investigation (2023)

BACKGROUNDAutoimmune diseases often have strong genetic associations with specific HLA-DR alleles. The synovial lesion in chronic inflammatory forms of arthritis shows marked upregulation of HLA-DR molecules, including in postinfectious Lyme arthritis (LA). However, the identity of HLA-DR-presented peptides, and therefore the reasons for these associations, has frequently remained elusive.METHODSUsing immunopeptidomics to detect HLA-DR-presented peptides from synovial tissue, we identified T cell epitopes from 3 extracellular matrix (ECM) proteins in patients with postinfectious LA, identified potential Borreliella burgdorferi-mimic (Bb-mimic) epitopes, and characterized T and B cell responses to these peptides or proteins.RESULTSOf 24 postinfectious LA patients, 58% had CD4+ T cell responses to at least 1 epitope of 3 ECM proteins, fibronectin-1, laminin B2, and/or collagen Vα1, and 17% of 52 such patients had antibody responses to at least 1 of these proteins. Patients with autoreactive T cell responses had significantly increased frequencies of HLA-DRB1*04 or -DRB1*1501 alleles and more prolonged arthritis. When tetramer reagents were loaded with ECM or corresponding Bb-mimic peptides, binding was only with the autoreactive T cells. A high percentage of ECM-autoreactive CD4+ T cells in synovial fluid were T-bet-expressing Th1 cells, a small percentage were RoRγt-expressing Th17 cells, and a minimal percentage were FoxP3-expressing Tregs.CONCLUSIONAutoreactive, proinflammatory CD4+ T cells and autoantibodies develop to ECM proteins in a subgroup of postinfectious LA patients who have specific HLA-DR alleles. Rather than the traditional molecular mimicry model, we propose that epitope spreading provides the best explanation for this example of infection-induced autoimmunity.FUNDINGSupported by National Institute of Allergy and Infectious Diseases R01-AI101175, R01-AI144365, and F32-AI125764; National Institute of Arthritis and Musculoskeletal and Skin Diseases K01-AR062098 and T32-AR007258; NIH grants P41-GM104603, R24-GM134210, S10-RR020946, S10-OD010724, S10-OD021651, and S10-OD021728; and the G. Harold and Leila Y. Mathers Foundation, the Eshe Fund, and the Lyme Disease and Arthritis Research Fund at Massachusetts General Hospital.